Research workbench
Structure of human endothelial nitric oxide synthase heme domain in complex with HW69
Analyse Structure of human endothelial nitric oxide synthase heme domain in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AV7
- Type
- protein
- Length
- 1,609 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitric oxide synthase, endothelial
- EC
- 1.14.13.39
- UniProt
- P29474
- Ligands
- HEM, H4B, W69, GD, ZN, CL
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitric oxide synthase, endothelial (EC 1.14.13.39) | protein | 404 | 40% helix, 15% strand | P29474 |
| B, D | Nitric oxide synthase, endothelial (EC 1.14.13.39) | protein | 402 | 41% helix, 14% strand | P29474 |
| C | Nitric oxide synthase, endothelial (EC 1.14.13.39) | protein | 401 | 41% helix, 16% strand | P29474 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- H4B · 5,6,7,8-tetrahydrobiopterin · ligand · 4 copies · chains A, B, C, D
- W69 · 6-(2-{3-[3-(dimethylamino)propyl]-5-fluorophenyl}ethyl)-4-methylpyridin-2-amine · ligand · 4 copies · chains A, B, C, D
- GD · Gadolinium atom · metal · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 2 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · 9 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1077 | 0.85 | 0.86 | 90 | HEM, H4B, W69, CL |
| 2 | 1043 | 0.85 | 0.86 | 82 | HEM, H4B, W69, CL |
| 3 | 1118 | 0.83 | 0.84 | 83 | HEM, H4B, W69, CL |
| 4 | 1170 | 0.83 | 0.84 | 96 | HEM, H4B, W69, CL |
| 5 | 87 | 0.71 | 0.95 | 20 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2748 Ų buried · 42 hydrogen bonds · protein-protein
- C–D · 2736 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 564 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 75 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6AV7 · Structure of human endothelial nitric oxide synthase heme domain in complex with HW69 · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P29474
- Elsewhere: RCSB PDB 6AV7 · PDBe 6AV7 · UniProt P29474
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